I have a similar issue... disabling Flux doesn't completely restore colours to normal. For that I have to disable and restart.
Other issues include the 'flashes' of full blue-ness at random intervals and the way the app sometimes stops running and you have to reopen it to get the warmer colours again.
Will you ever be able to issue updates to the side loaded version on non jailbroken devices?
I'm using an iPhone 6 running iOS 9.1